SMTL ID : 8gr8.1

Crystal structure of peroxisomal citrate synthase (Cit2) from Saccharomycescerevisiae

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.39 Å

Oligo State

homo-dimer

Ligands

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 5 residues within 4Å: Chain A: N.261, V.262, H.293 Chain B: I.438, R.440 Ligand excluded by PLIP CL.2: 5 residues within 4Å: Chain A: I.438, R.440 Chain B: N.261, V.262, H.293 Ligand excluded by PLIP

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 2 residues within 4Å: Chain A: W.325, E.382 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.382 GOL.4: 6 residues within 4Å: Chain A: I.33, H.37, R.87, L.117, T.118, T.430 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.87, A:R.87, A:T.118, A:T.430 GOL.5: 4 residues within 4Å: Chain A: H.156, A.289 Chain B: E.169, A.175 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:A.289, B:E.169, B:E.169 Water bridges: B:S.276 GOL.6: 4 residues within 4Å: Chain A: Y.373, E.374, P.377, W.390 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.373 GOL.9: 2 residues within 4Å: Chain B: W.325, N.329 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.329 GOL.10: 3 residues within 4Å: Chain B: Y.373, E.374, P.377 No protein-ligand interaction detected (PLIP)

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.7: 7 residues within 4Å: Chain A: D.242, H.359, F.360, P.361, D.362, Y.363, Y.403 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.362, A:Y.363

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.8: 8 residues within 4Å: Chain A: L.78, H.257, H.339, A.340, V.341, L.342, D.346, R.348 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.340, A:V.341, A:L.342, A:R.348 Water bridges: A:N.392 PEG.11: 9 residues within 4Å: Chain B: L.78, G.83, I.84, H.257, H.339, L.342, D.346, P.347, R.348 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:I.84, B:H.339, B:R.348 Water bridges: B:A.340

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nishio, K. et al., Defective import of mitochondrial metabolic enzyme elicits ectopic metabolic stress. Sci Adv (2023)

Release Date

2023-04-26

Peptides

Citrate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Citrate synthase

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